Contacts of the helix formed by residues 329 - 340 (chain L) in PDB entry 3J8B
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 329 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323L TYR* 4.7 5.6 - - - -
324L LEU* 6.1 1.1 - - - +
327L ARG 3.6 4.0 + - - +
328L ARG* 1.3 70.8 - - - +
330L GLN* 1.3 62.9 + - - +
331L ASP 3.5 1.8 - - - -
332L ALA* 4.0 4.0 + - - +
333L ILE* 3.1 24.7 + - - +
374L ALA* 4.0 30.2 - - + +
377L MET* 4.4 15.5 - - + -
378L TYR* 5.1 5.5 - - - +
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Residues in contact with GLN 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328L ARG* 3.3 9.7 - - + -
329L TYR* 1.3 81.3 - - - +
331L ASP* 1.3 64.4 + - - +
333L ILE* 3.3 7.2 + - - +
334L ARG* 3.3 19.6 + - - +
378L TYR* 5.8 2.7 - - - +
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Residues in contact with ASP 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L VAL* 5.2 3.2 - - - +
323L TYR* 4.3 10.2 - - + +
328L ARG* 4.8 5.5 + - + +
329L TYR 3.5 0.6 - - - -
330L GLN* 1.3 79.3 - - - +
332L ALA* 1.3 56.8 + - - +
334L ARG* 3.5 7.8 + - - +
335L VAL* 3.3 24.7 + - - +
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Residues in contact with ALA 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319L VAL 4.2 1.1 - - - -
320L GLY* 3.2 29.1 - - - +
323L TYR* 2.3 40.9 - - + +
324L LEU 4.3 0.4 - - - +
329L TYR* 4.2 5.4 - - - +
331L ASP* 1.3 71.4 - - - +
333L ILE* 1.4 65.0 + - - +
334L ARG 3.3 0.2 - - - -
335L VAL* 4.1 1.3 - - - +
336L PHE* 3.0 28.8 + - - +
374L ALA* 5.0 12.6 - - + -
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Residues in contact with ILE 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329L TYR 3.1 22.1 + - - +
330L GLN* 3.3 9.2 + - - +
332L ALA* 1.4 76.1 - - - +
334L ARG* 1.3 61.3 + - - +
336L PHE* 4.0 4.0 - - - +
337L ALA* 3.2 23.7 + - - +
342L TYR* 5.3 1.0 - - - +
371L LEU* 6.4 0.7 - - - -
374L ALA* 5.1 8.7 - - + +
375L LEU* 5.6 2.7 - - - +
378L TYR* 4.4 19.3 - - + -
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Residues in contact with ARG 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330L GLN 3.3 9.1 + - - +
331L ASP* 3.7 9.9 - - - +
332L ALA 3.3 0.6 - - - -
333L ILE* 1.3 75.8 - - - +
335L VAL* 1.3 63.2 + - - +
337L ALA* 3.4 5.7 + - - +
338L ASN* 3.1 23.4 + - - +
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Residues in contact with VAL 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316L TYR* 2.9 32.9 - - - +
319L VAL* 3.3 34.5 - - + -
320L GLY 4.2 1.3 - - - +
331L ASP 3.3 12.7 + - - +
332L ALA 4.1 3.1 - - - +
334L ARG* 1.3 76.5 - - - +
336L PHE* 1.4 56.9 - - - +
338L ASN* 3.4 7.0 + - - +
339L ILE 3.0 13.9 + - - -
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Residues in contact with PHE 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316L TYR 4.2 6.3 + - - +
317L TYR* 6.0 0.9 - - - +
320L GLY* 5.4 4.9 - - - -
332L ALA 3.0 19.3 + - - +
333L ILE* 4.0 4.0 - - - +
335L VAL* 1.4 74.9 - - - +
337L ALA* 1.4 54.0 + - - +
339L ILE* 3.3 7.6 + - - +
340L LEU* 2.6 37.2 + - - +
367L MET* 5.3 4.7 - - + +
368L HIS* 6.0 0.9 - - - -
371L LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333L ILE 3.2 16.4 + - - +
334L ARG* 3.4 5.8 + - - +
336L PHE* 1.4 74.9 - - - +
338L ASN* 1.3 60.2 + - - +
340L LEU 1.6 37.5 - - - +
341L LEU* 3.3 3.1 + - - -
342L TYR* 3.1 33.9 - - + +
350L PHE* 5.5 3.0 - - + +
352L ARG* 5.0 0.7 - - - +
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Residues in contact with ASN 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316L TYR* 5.3 1.6 - - + -
334L ARG 3.1 13.2 + - - +
335L VAL* 3.6 10.5 - - - +
337L ALA* 1.3 78.4 - - - +
339L ILE* 1.3 63.1 + - - +
340L LEU* 4.4 0.3 - - - -
352L ARG* 5.0 4.5 - - - +
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Residues in contact with ILE 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312L GLN 5.4 0.9 - - - -
313L VAL* 3.9 27.6 - - + +
316L TYR* 3.0 31.7 - - + +
317L TYR* 4.7 0.9 - - + +
335L VAL 3.0 5.3 + - - -
336L PHE* 3.6 9.4 - - - +
338L ASN* 1.3 77.6 - - - +
340L LEU* 1.3 61.1 + - + +
352L ARG* 4.4 6.2 - - - +
364L ASN* 4.7 11.8 - - + +
367L MET* 6.0 6.3 - - + -
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Residues in contact with LEU 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336L PHE 2.6 14.0 + - - +
337L ALA* 1.6 45.8 - - - +
339L ILE* 1.3 76.2 - - + +
341L LEU* 1.3 59.2 + - - +
352L ARG* 3.9 7.6 - - - -
364L ASN* 4.3 14.8 - - + +
365L GLU* 6.1 0.2 - - - -
367L MET* 6.2 0.4 - - + -
368L HIS* 4.2 25.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il